Pokémon Reset Bloodlines: Cipher Interlude
by Viroro-kun
Summary: Spin-off of Pokémon Reset Bloodlines by Crossoverpairinglover. Cipher, the secret organization of the Orre region, is gathering Pokémon to achieve their objectives. During one of those missions, however, a newly inducted Peon questions their actions. [Knowledge of the main story is suggested, but not essential]


No Pokémon was invincible: that was one of the absolutes of Pokémon battling, and a rule every trainer eventually ran into. Even Pokémon with supposedly almost perfect coverage like Spiritomb and Sableye had a crippling weakness one could exploit.

It was something that Ein had heard many, many times. And no matter how much people claimed that, he knew that a way to create a truly invincible Pokémon existed, and after several years he had finally succeded. He had to share a slice of the glory with Lovrina, sure, but she had only refined a process he theorized and created. If it weren't for him, Cipher would have never obtained its ultimate weapon: Shadow Pokémon, the ultimate fighting machines capable of hurting every single Pokémon bar themselves for supereffective damage.

The process still had many kinks to fix of course, between erratic behavior and very slim possibility of reversal, but the work on the SD series of experiments was proceeding as smoothly as it could, and work on the prospective XD series became more feasible with each passing day.

Ein was incredibly grateful to Cipher for giving him the chance to expand upon his theories, and demonstrating his Shadow Pokémon's superiority as Cipher slowly conquered the world was a nifty little bonus. A bonus that made all the logistics involved and inter and extra group politics way easier to swallow. Like the discussion he was having with Chief Admin Nascour from the Shadow Pokémon Lab, for instance.

"Evice is wondering when his personal Shadow Pokémon will be ready, Ein." The gray-haired man stared at him, arms folded.

Ein took off his glasses and wiped them. "The process is going smoothly, even if it will take time: thoroughly breaking the will of a Pokémon is essential before the process can be enacted, and Tyranitar are prideful Pokémon. For one of my superiors, anything less than perfection won't do."

"I admire your dedication, but you should definitely work on accelerating the Shadow Pokémon production. That run-in Lovrina had with Driftveil's Gym Leader proved that SD0014 is capable to push an expert trainer in a corner, and we need more like it."

"Which is why we have to prioritize quality over quantity. Each Shadow Pokémon is a work of art on its own, trying to craft them quicker would just cause them to become inefficient." Ein raised an arm, grinning. "I am sure the next contingent of Pokémon the Peons will bring from Unova will provide us with good material for further Shadow Pokémon, in any case. The region's unique Pokémon might give us an edge to keep our power in Orre and expand in other regions."

Nascour stood still, before turning around. "I see your point. I will ask for your report once you receive the next batch of Pokémon: until then, I expect production to continue as scheduled."

The comunication closed and the screen went black. Ein took a deep sigh and rose from his chair, walking further down his lab where the latest test subjects were waiting, looking forward to the next batch as well. He had always been interested in studying a Sawsbuck.

* * *

 _It was a quiet day in Unova. In a small forest near Floccesy Town, known by a select few as Pledge Grove, two young boys were having a Pokémon battle: a Snivy against an Oshawott in full samurai attire._

 _"Sir Thorn, Vine Whip!" A brown-haired boy called, pointing onward._

 _His opponent, a black-haired kid, did the same. "Mizutaro, Razor Shell!"_

 _Sir Thorn and Mizutaro went at each other, water blade meeting sharp vines. They clashed several times, until Sir Thorn placed a vine near Mizutaro's feet: the Oshawott tripped, and Sir Thorn slapped him on the nearby rock, knocking him out._

 _"We won!" The brown-haired boy yelled, sharing a high-five with Sir Thorn._

 _The other boy grabbed the defeated Mizutaro, sighing. "That's not fair, Shawn. You and Sir Thorn have the type advantage! Of course we lost!"_

 _"Sure, sure. Keep telling yourself that Jeff."_

 _Jeff puffed his cheeks. "Jerk."_

 _"Likewise." Shawn smirked._

 _Jeff and Mizutaro folded their arms at once. "Once we actually start our journey, we are going to kick your butt all the time!"_

 _Hearing that, Shawn paused and turned his head down, Sir Thorn's face darkening as well. Jeff and Mizutaro approached the two, giving them puzzled looks._

 _"Uhm, about that." Shawn scratched his neck, gulping. "There's something I wanted to tell you."_

 _"What is it?"_

 _Jeff tilted his head._  
 _  
Shawn took a deep breath, looking back at Jeff. "I was planning to start my journey in the Orre region. The Vertress Conference just flat out sucks, while Orre has many cool facilities. There's even a mountain of one hundred strong trainers where Ho-Oh is rumored to reside! You can't beat that!"_

 _Jeff flinched, almost dropping Mizutaro; trainer and Pokémon pulled themselves together, staring worriedly at their friends._

 _"Shawn, you are joking, right?" He asked, paling._

 _"Absolutely not." Shawn and Sir Thorn shook their heads at once. "I don't want to diss our League too much, but Vertress gotta be one of the lamest regional Conferences. They can't even afford different fields, come on! If me and Sir Thorn want to become the strongest, we need to undertake much better challenges, and Orre is the real deal."_

 _"Orre is also a crime-ridden hole that everyone is ashamed of. There's a reason people pretend that region doesn't exist!"_

 _Shawn shrugged. "Meh, people say the same about Castelia City. You shouldn't believe everything you hear."_

 _"Well, sorry if I'm worried for you." Jeff's expression darkened, clenching his fists. "We said we'd go to a journey together, me and Mizutaro and you and Sir Thorn. Do we matter so little for you two? Our regional League is not even that bad."_

 _"It's not that, I told you." Shawn faced downward._

 _Jeff scoffed. "It doesn't look like it."_

 _Mizutaro glared at the two and turned the other way, as Sir Thorn groaned._

 _Shawn sighed, looking away from the angry Jeff and Mizutaro. He scratched his head as he let his eyes wander, until he noticed the large rock with four slashing marks at their side, the one where the Swords of Justice were rumored to have done their own vow to protect Pokémon. At that point, Shawn and Sir Thorn flinched and looked at each other, grinning as an idea wormed its way in their heads._

 _"Say, this place is the Pledge Grove, right? Then, why don't we do our own pledge?" Shawn asked, placing a hand on the slashed rock._

 _Jeff and Mizutaro blinked. "What do you mean?"_

 _"Once our journeys are over, we will meet again here and see who became the best trainer." Shawn offered a handshake with a smile. "What do you think?"_

 _Jeff pondered for a while, glancing Mizutaro. Then, he sighed and shook his head._

 _"I dunno." Jeff grinned. "Wouldn't it be unfair for you to face the next Unovan League Champion without due preparation?"_

 _Shawn chuckled, punching Jeff's shoulder lightly. "Like that'd ever happen!"_

 _"It totally will! And I will wreck you!" Jeff replied in kind, giggling._

 _Shawn beamed, giving him a confident smirk. "Alright then. I look forward to see it!"_

 _The two boys shared another laugh, before shaking their hands and accepting the pledge; near them, Sir Thorn and Mizutaro did the same. All four of them were ready to become the very best, like no one ever was._

* * *

"Hey, Peon! Are you listening or not?"

Shawn flinched, heart racing as he turned around: all the other Peons, armored head to toe just like him, were staring in his direction. In front of him stood Exol, his large and muscular Commander, glaring daggers from behind his visor.

He tapped his foot, waiting. "Well?"

"S-sorry, I was distracted and didn't listen." Shawn gulped, looking down.

He felt Exol's cold stare on him for quite a while before he scoffed and turned away. "Figures. Then again, you are one of Dakim's guys. I expected you to be a dimwit."

Shawn heard the other Peons laugh at him, and he rubbed his shoulder wordless. Exol sighed, and faced the Peons again.

"Since the princess here didn't listen, I will repeat myself: we are here to capture as many Pokémon as possible. They are all ones you don't see in Orre normally, so just take all you can. If anyone from that ranch or the nearby cities gets too nosy, we are allowed to use lethal force. Understood?"

All the Peons sans Shawn erupted in a loud "Yes!". Exol grinned and turned around, walking away.

"Very well then. Now don't waste time, and get to work!"

All the Peons struck a military salute and quickly scattered while summoning their Pokémon, immediately starting to round up the wild ones around them. Shawn watched for a short while, before sighing: after what happened, he definitely couldn't slack off on his 'job'. He tossed two Poké Ball, and a battle-worn Servine and Mandibuzz appeared in front of him.

"We need to get as many Pokémon as possible. Let's get to work," Shawn said. The Servine nodded, while the Mandibuzz just flew away without a word: Shawn knew her enough to be aware that she listened.

The Servine tilted his head at Shawn, extending a vine at his face and rubbing it. Shawn gave a sad smile, petting his head.

"I'm okay Sir Thorn, I really am. Let's just get to work now, I don't want Commander Exol to yell at me again." Shawn moved away the vine, staring at his starter. They both nodded, and started searching together.

As they mindlessly worked and helped with the captures, Shawn let his thoughts run wild. Helping criminals? Long ago he would've found it unthinkable, and yet here he was. And he only had himself to blame for his current predicament, himself and his overconfidence.

He and Sir Thorn thought challenging Orre's facilities would've been tough, but doable; they didn't expect the region itself to be almost impossible to live in.

While Phenac City was a decent enough place, the nearby Pyrite Town truly lived up to how Jeff described the region: with a grand amount of two cops in the whole town crime was rampant, the local Colosseum was in shambles, and ante battles dominated over regular ones.

His first mistake when he reached it was challenging a trainer they called "Burning Earth" Dakim, which defeated Sir Thorn in less than five seconds flat. As a result, he had lost most of his money, and had to live on the streets and almost starve with no way to even leave Pyrite Town, let alone Orre. With next to no money and way too strong opponents, Shawn had to resort to steal some stuff from the local PokéMart and visitors of the town to stay afloat. In such harsh conditions, Shawn and Sir Thorn trained: they became stronger, and eventually Sir Thorn evolved into a Servine while he caught one of the roaming Mandibuzz of the region, calling her Selvaggia. That helped some and they managed to win back some of what they'd lost, but life was still harsh.

That was when he saw the offer. There was an announcement looking for strong trainers, and he and Sir Thorn applied for it. They assumed it would've been something akin to a bodyguard job, escorting someone to another city, or something in that vein.

Instead, they found themselves inside one of Pyrite's many decreipt buildings alongside several other trainers. The doors were locked behind them, and they were ordered to fight each other: hearing that, everyone started battling in a heartbeat. Sir Thorn and Selvaggia had a hard time managing all the opponents, but eventually he became one of the few trainers still standing when they ordered them to stop. They were then led on a different room, and to their surprise Burning Earth Dakim was behind it.

The purpose of the improvised battle royale was made clear: it was a recruitment drive, for an organization called 'Cipher'. They were given the chance of joining the organization, or rather gave them no options: after telling them all they needed to know, they were given the Peon uniform and dispatched for a brief training session, and then sent away on their first missions. It all happened so fast that Shawn had almost no time to dwell on it.

Shawn sighed. Jeff was always right, and he should have listened more to him.

"Hey, Peon! What, did you forget to sleep or something? Get to work again!" Exol yelled; Shawn tensed up, nodded twice, and went back to rounding up Pokémon.

Giving a quick look around, he could see that the other Peons had managed to round up about two dozens Pokémon, mostly common ones like Patrat, Pidove or the imported Mareep of Floccesy Ranch. Far from enough for Cipher's interests, with most even managing to slip away.

"What's taking you all? Is this the best you can find?" Exol sneered, then grabbed a Poké Ball. "Guess I need to show you how to catch a Pokémon properly. Go, SD0015!"

The Poké Ball was thrown, and a Mawile appeared at Exol's side. An emotionless, uncannily still Mawile.

Sir Thorn and Selvaggia instantly felt a chill running down their spines, taking defensive stances. All the other Peons' Pokémon did the same, all glaring and stepping back from the Mawile. Shawn frowned, observing it as well. He had heard of those: 'Shadow Pokémon', as his Cipher instructors had called them. They didn't tell them much during training, only that they were the ultimate tool of Cipher and that only high ranking members of the organization were allowed to use them.

As he kept looking, Shawn received the same chill his Pokémon did. He had never liked Fairy-types to begin with, but even for their standards that Mawile felt _wrong_.

"Now SD0015, track down any strong Pokémon around, and bring them here!" Exol yelled, pointing onward.

Wordless, SD0015 dashed on towards the tall grass, charging something. They all felt a cold breeze, and several Pokémon fell exhausted from trees and grass: Sewaddle, Purrloin, even rare ones like Venipede and Audino.

Exol grinned. "Keep going, SD0015."

With nary a nod, SD0015 kept charging nothing, making Pokémon fell with ease. It couldn't even be called a fight: no matter what the Mawile did, it was strong enough to instantly defeat anything on its path. Some brave Pokémon sometimes tried to challenge it, only to be swatted away into the pile with all else. Nothing seemed to faze it.

Watching on, Shawn and Sir Thorn grew even more terrified: even with some Pokémon being more violent than others, none they had ever seen acted in such a detached, automatic way. What exactly did they do to it to turn a Mawile into that?

Exol stared proudly, turning at the Peons. "This is the true power of Cipher. With these Pokémon, the world shall be ours. Nothing will ever go wrong!"

As he said so, SD0015's body went still, freezing in place. The Peons and Exol turned to it, the latter frowning.

SD0015 widened its eyes as they became bloodshot. Then, a wicked grin formed on both its mouths. It charged its attack again, hurting the already downed opponents instead of new ones.

Exol stepped onward. "What the hell are you doing, SD0015? You don't need to attack them!"

SD0015 stopped attacking, only to turn towards Exol. Its grin widened as it charged again.

Exol sweated cold, instantly grabbing a Poké Ball. "Raichu, use-"

A wave of nothing sent the Cipher Commander crashing on a tree: he yelled and held his back, while his Poké Ball rolled away from him.

"Commander!" yelled several Peons, trying to help him.

Exol shot them all down with a glare. "Don't care about me! Stop it!"

The Peons froze and gave a shaky nod, turning to their Pokémon and directing them all towards SD0015. The Shadow Pokémon barely even looked at any of them before knocking them away with its special attack, sending almost all Peons and Pokémon back several steps with little effort.

Still unharmed, Shawn and his Pokémon felt a cold shiver as SD0015 turned and dashed in their direction. They were going to be next, and they needed to act now.

Shawn clenched his fists, sharing a nod with his team. Then, he pointed onward. "Sir Thorn, block it!"

A vine extended from Sir Thorn, grabbing SD0015 by its second maw. With enough force, Shawn's Servine pulled it skyward and crashed it on the ground; it sent a yell, and Shawn winced.

He shook his head and turned to his Mandibuzz. "Selvaggia, Brave Bird!"

A blue aura flared around Selvaggia as she charged at the Shadow Pokémon. SD0015 raised again and stared emptily at Selvaggia, only to charge her itself, without any visible aura.

Selvaggia and SD0015 clashed, and the Mandibuzz tasted the dirt. Sir Thorn tried to push the Shadow Pokémon back down, only for SD0015 to pull him closer and drag _him_ down.

Shawn bit his lip. "Sir Thorn, quick! Vine Whip!"

Sir Thorn tried whipping with his extended vine; SD0015 bit onto it with its second maw, bringing him up close. The Mawile grinned, and tackled Sir Thorn to the ground.

Then, it started hitting it with that weird attack and its claws, over and over. Sir Thorn tried to retaliate and escape, but SD0015 just pressed him down harder. Soon, scrapes gave way to gashes, and blood started to flow down Sir Thorn's face.

Shawn paled, and sprinted without second thoughts. He had to do something, and now!

He tackled down SD0015 himself, freeing Sir Thorn. He pressed his body close to it, and then embraced it softly. It tried breaking free, but Shawn resisted the attempts.

"Stop, SD0015! You don't need to attack us!" He kept it close, tightening his grip on it. "Please, SD0015!"

SD0015 trashed and yelled, biting into Shawn's shoulder as it tried blowing him back. All the Peons, Exol and his Pokémon looked on, puzzled and bewildered. Shawn's body slowly became littered of bites and scars, but he still didn't yield.

"Mawile, please!" Shawn held it tighter, swallowing down the pain. "There's no need for this violence, Mawile!"

Hearing that name over and over made something click in SD0015's mind; it suddenly stopped moving, turning towards its surroundings. It then gave a quick, brief smile towards Shawn before returning to its previous emotionless expression, still and quiet as earlier.

Sir Thorn wiped the blood off his face as he stared at Shawn and Mawile with a puzzled glance. Selvaggia and the Peons did likewise.

Exol raised and approached SD0015 while Shawn moved aside. After staring for several seconds, he rubbed his chin.

He then faced Shawn, arms crossed. "SD0015 seems back to normal. You did a good job."

"H-huh, thanks, sir." Shawn rubbed his shoulder, a small smile on his face.

"However..." Exol's glare fiercened, stepping closer. "Don't you dare doing that again. You might've messed with its programming and ruined one of Cipher's greatest assets."

Shawn paled, then nodded a couple times. "I-I understand."

"Good. Now, patch your bruises and get back to work!" Exol yelled, frowning.

Shawn gave another nod, quickly grabbing the still bleeding Sir Thorn while Selvaggia soared above them. Shawn knew exactly where to go to heal up his friend and rest up a bit, distant from all the madness he had been involved with.

* * *

Returning to Pledge Grove gave Shawn a strange feeling; it felt like his memories of it came from an entirely different life, and standing there again just seemed unnatural. However, it was the closest place to home for him, and after all that happened he needed someplace familiar to stay in, if only briefly.

"Stay still." Shawn slowly wiped the blood off Sir Thorn's face; the Servine winced, but tried to comply. The Mawile's claws dug deep on his skin, and even after healing Sir Thorn would most likely keep a scar over his left eye.

After cleaning his starter and placing a bandage over his eye Shawn sighed and took off his helmet, glancing skyward. Sir Thorn did the same, while Selvaggia left to find some food.

Shawn frowned, balling his fists. There were still many things he didn't know of Cipher, but it was clear that they weren't up to anything good. He had to leave before it was too late. He looked around: he had never been this close to home since he started his journey. Aspertia City wasn't too far, and his friends and family could've probably helped him out.

He grabbed his forehead, shaking his head. No way Cipher wouldn't connect the dots, and he couldn't endanger the people he cared about. Fleeing there was not an option.

Shawn let himself fall down the grass, grabbing Sir Thorn close to his chest. He let his mind wander as he stared at the clouds above.

Or at least he tried to, before something tackled him and Sir Thorn down the grass, rolling around before crashing on a tree trunk.

"Ah!" Shawn yelled, slowly standing again as he rubbed his back, his Servine mimicking him. They frowned onward. "What the heck-"

They stopped the moment they saw who tackled them: a small Dewott, wearing a full samurai garb and a big smile, waving at them.

Shawn blinked twice, squinting. "Wait a minute. You are..."

"Mizutaro! I told you to not run away like this!"

Shawn flinched and widened his eyes as he heard the voice: turning its way, he saw another kid around his age, with black hair and an eyebrow raised. Shawn gulped: he was taller and older, but he recognized him straight away.

"Jeff?"

The other tilted his head. "Shawn?"

Shawn nodded. Jeff beamed in response, and tackled him into a hug.

"You finally came back, you dummy! We were starting to get worried here!" He tightened the hug, his smile growing wider. "You could've called or something every once in a while!"

Shawn chuckled, forcing a smirk and rubbing his neck as he slipped out of the hug. "S-sorry, Orre has rather poor reception. I didn't mean to worry you."

"That's okay, I'm just glad to see you back." Jeff stepped behind, noticing then Shawn's armor. He frowned. "What's with the funky outfit, though? You seem to be part of some kind of army now."

"Oh, this?" Shawn grimaced, quickly pondering and sweating. "It's just... what people considered 'Ace Trainers' wear in Orre, that's all. I thought I'd have to blend better there."

Jeff stared blankly at his friend, checking the armor again. He raised an eyebrow once more. "Orre's fashion is _weird_."

"Trust me, there's lots of weird in Orre." Shawn gave a small grin, turning back to Jeff's Dewott as he talked with Sir Thorn. "I see Mizutaro evolved at last."

"And I see Sir Thorn did as well." Jeff folded his arms. Then, he saw Selvaggia approacing them again with a freshly caught Patrat in her maws, landing near Shawn. "And you caught a Mandibuzz too? Neat!"

"Not as impressive as it might seem, really. Mandibuzz are pretty common in Orre." Shawn gave a small smile, as Selvaggia frowned his way. He then turned back to Jeff and his starter. "It must've been hard to win eight badges with Mizutaro staying a Dewott, though."

Hearing that, Jeff clenched his fists for a second, sighing. He and Mizutaro scratched their heads at once, trading stares before looking back at their friends.

"Ehm, about that..." Jeff took a deep breath, then closed his eyes and faced downward. "After four badges me and Mizutaro didn't manage to defeat any Gym Leader at all, so we quit and back to Aspertia. I've got a small job right now, and Mizutaro is helping out."

"What?" Shawn frowned.

Jeff chuckled, sighing right after. "The League circuit turned out to be harder than we expected and we had to drop out." He put his hands behind his head. "I'm a bit annoyed not to have made it far, but I still like to have tried it. Me and Mizutaro had plenty of fun on the way."

Shawn adjusted his scarf, turning away. He wasn't the only unlucky one, it seemed.

"Sorry to hear that."

"No need to be." Jeff shrugged. "It's a bummer to think you went better than me, though. Seems like you were right in the end."

Shawn shot a glance at Sir Thorn, hesitating to speak. Sir Thorn gave Shawn a firm nod as he locked into him, and the trainer took a deep breath.

"About that, I-"

"Oh, don't misunderstand me." Jeff wiggled his finger, grinning alongside Mizutaro as they crossed their arms at once. "I might not be a trainer anymore, but I still want to do our battle."

He pointed onward, as Mizutaro took a stance and unsheated his Scalchops. "Prepare to fight!"

As the gauntlet was thrown, Shawn could hear some steps in the distance. His body stiffened, then quickly ran to Jeff and grabbed his shoulders.

"Jeff, please, listen to me." He gulped, staring into Jeff. "Now's not the time for this, it's dangerous."

Mizutaro scratched his head with the Scalchops, and Jeff gave him a puzzled look. "What do you mean?"

Shawn grimaced, breaking eye contact. "I need to tell you something, I-"

"Where have you gone, stupid Peon? Get back to work!"

Shawn's heart skipped a beat, paling and tensing up as he turned around to see Exol and the other Peons reaching them. His Pokémon got ready to fight. Exol turned around, then grinned their way.

"Oh, you were. Good job." He pointed onward. "We will give you a hand here. Surround him!"

The Peons grunted, circling around Shawn and Jeff. Shawn grimaced, clenching his fists.

"What's going on? Who are these people?" Jeff asked, shooting glances all around.

Shawn bared his teeth, pointing somewhere. "Jeff, go! Now!"

Staring at Shawn's pale face, Jeff understood; he nodded and tried to escape, only to find several Pokémon pushing him back in the middle. Shawn was about to order Sir Thorn and Selvaggia before remembering who was in front of them, pausing and biting his lip.

Jeff glared. "Mizutaro, use-"

He stopped when he saw that his Dewott wasn't close by. He searched, mouth agape.

"Were you looking for this guy?" Exol asked, holding Mizutaro by the scruff of its clothes. The Dewott was fuming, waving his arms and Scalchops around.

Jeff widened his eyes, then the Peons tackled him on the ground, hands grabbing all the belongings they could find. A Peon rose right after, holding six Poké Balls.

"We got all his Pokémon, sir!"

"Excellent." Exol nodded, then turned to Shawn. "Now, get rid of him. He's a dangerous witness."

Shawn stood still, observing Jeff under the Peons. He rubbed the sweat off his face, and tried putting on a frown.

He shook his head. "I-I can't."

"Pardon me?" Exol stepped closer. "I think I heard the wrong reply."

Shawn's confidence melted away, the frown replaced with a grimace once more.

"S-Shawn, what's g-going on?" Jeff asked, pained and on the ground as the Peons got off him.

Jeff's pale face and Exol's frown kept alternating in Shawn's vision, sweat pouring on his face and his whole body trembling. Mizutaro, Sir Thorn, Selvaggia, the Peons, Exol and Jeff again: his eyes just wandered everywhere, searching for an answer.

He had only one choice. It had to be the right one. Jeff had done nothing wrong, he didn't have to end up there.

Shawn gulped, feeling Exol behind him. He saw how powerful SD0015 was, and noticed the Commander keeping a hand on his Poké Ball. He turned back to Jeff, on the ground and harmless. Both he and Mizutaro were sending pleading looks, asking to be helped. Sir Thorn was as unsure as he was.

Shawn gulped again. He had only one choice. And he choose himself.

"I am sorry." Shawn gulped and closed his eyes, failing to stop shaking.

He pointed to his friend, and gave his order.

* * *

"I thought you said you would report right after the next batch arrived, Ein." Nascour's crimson eyes pierced through the screen, right at the scientist.

Ein shrugged, holding a Poké Ball with 'SD0016' embedded on the button. "Did I? I am sorry, I went straight to work the moment I received the new Pokémon. There was a fun one that acted all defiant, but broke in nothing. It's got to be the fastest Shadow Pokémon I ever produced. I predict I will be able to obtain at least four other Shadow Pokémon from the batch."

"That's good to hear, but there's something important we have to talk about." Nascour placed his arms akimbo. "It appears SD0015 went berserk during the mission, just like many of the other SD series specimen did. I believe Lovrina called it 'Reverse Mode'."

Ein sharpened his glance, shaking his head. "That's what she calls it, and it's just a tentative name. I prefer 'Hyper Mode', myself."

"Regardless of how it's called, it's a dangerous variable. Cipher can't rely on unstable weapons."

Ein shrugged. "It's sadly an inherent risk when it comes to Shadow Pokémon: the process to close off their hearts also makes any inkling of emotion turn them erratic. It's a programming flaw me and Lovrina hope to excise as we move towards the XD series."

"You and Lovrina need to refine the process." Nascour stared him down. "And there's another thing you should be aware of. You and Lovrina made it so Shadow Pokémon could only use Shadow moves, right?"

Ein nodded. "In theory, yes. Knowledge of different moves is locked away, while others are enhanced into Shadow moves."

"I see. It is quite odd, then, that some Shadow Pokémon have reportedly relearned some if their locked up moves." Nascour's glare fiercened, and he crossed his arms. "Why did that happen, Ein?"

Ein frowned, adjusting his glasses as he turned down. After a few moments of thinking, he met Nascour's glare once more. "It might have something to do with the care the Peons employing them put them under. Transfer of positive emotions might be disrupting the process, and undoing it."

Nascour dug his nails in his arms, breathing in as his eyes pierced into Ein.

"This is a worse risk than Shadow Pokémon simply going berserk; Shadow Pokémon's advantage is that their attacks can't be seen with the naked eye. If that advantage is lost, then it is futile to deploy them."

"I agree." Ein massaged his chin, tapping on the keyboard to bring up some files in the meantime. "As I said, the fault most likely lies in some Peons getting too attached to the Shadow Pokémon they work with, treating them like a normal Pokémon would be. How did SD0015 snap out of Hyper Mode?"

"The report indicates that a Peon got close and called its species' name repeatedly. This calmed it down and brought it back to standard functioning."

After reading some notes, Ein nodded. "As expected. The only way to solve an imbalance of emotions is by adding more positive emotions. However, this causes the Pokémon to think it's a worthwhile creature, and not the tool it's meant to be. It brings the Shadow Pokémon back to standard functioning, but at the same time weakens the hold of the Shadow process."

"Does that mean care and compassion can turn a Shadow Pokémon back into a normal one?"

Ein shook his head. "Not quite, my process ensures a Shadow Pokémon can't turn back to normal on its own. However, it does still cause anomalies that hamper the regular efficiency of Shadow Pokémon, as we have seen."

Nascour closed his eyes for a second. He muttered something, then went back to Ein.

"All because some Peons decided to be nice." Nascour's glare sharpened. "Emotions are such a hindrance. I was starting to think about applying the Shadow Pokémon process to our Peons as well, ridding them of anything aside from their desire to help Cipher prosper. They are useless beyond that. Would that be possible?"

Ein rubbed his chin once more, adjusting his jacket and coat as he let his mind explore the possibility. After some seconds, however, he shook his head.

"While I can see the merit in it, I think it would quickly become inefficient. It would require us to subject all of our current Peons to the process beforehand, which would have to happen concurrently with the Shadow Pokémon project and consequently slow down both, leaving Cipher short on manpower and weapons. It may sound neat on paper to have Peons completely devoted to Cipher's cause, but the logistics involved are just not affordable without slowing down Cipher's operations to a crawl. I'd suggest not pursuing this option, Chief Admin."

Nascour nodded and turned around, breaking eye contact. "If you say so, we will put the project aside for now. However, we still need to find a way to avoid problems like this from coming up in the near future."

"That won't be a concern." Ein grinned, observing his Pokè Ball once more. "There are many ways to make sure humans follow a certain behavior. And I have the perfect reward in mind for our brave Peon..."

* * *

Back in Cipher's Headquarters Shawn was sitting in his room, staring blankly at his hands. Sir Thorn tried nudging him for attention, while Selvaggia sulked away from them.

Shawn shook his head, hands on his face. He had many options, and yet he choose the most selfish one. Why did he do it? Why did he choose himself over Jeff?

He fought back the tears, his head feeling heavy. This was all his faut, from beginning to end, all because of his damn ego. He was nothing but an useless idiot.

Shawn yelled and punched the opposite wall, over and over; Sir Thorn sighed and grimaced. Shawn only stopped when his hands started to hurt, shaking his now red fists. Shawn might've gone further if the door didn't open without warning.

"Hey, Peon!"

Shawn, Sir Thorn and Selvaggia jumped in place, quickly striking a military salute.

"Y-yes, Commander Exol, sir?" Shawn gulped, sweating.

"It's your lucky day." Exol grinned, searching in his armor's pouches. "The higher-ups told me that after your showing today you've become worthy of your very own Shadow Pokémon. Here."

He tossed a Poké Ball to Shawn; he clumsily caught it, giving Exol a confused look.

"It's one of the Pokémon of our batch, too. I'm sure you will like it." Exol turned away. "Get used to it, it might come in handy in your next mission."

The door closed behind him, and Shawn was again alone with his Poké Ball. He glanced at the device right after: it was completely like a regular Poké Ball, except for the 'SD0016' embedded in the central button.

Shawn then frozen, thinking back to Exol's words. This was a Pokémon they had caught. He sweated cold, hands trembling as he went back to the Poké Ball.

He gripped it tightly, taking a deep breath. They caught several Pokémon, and there was no guarantee it had to be _him_. It was probably a Pidove, maybe a Venipede.

Shawn shook his head. He had to know. He breathed in again, steadied himself, and threw the Poké Ball in the air.

His Shadow Pokémon appeared, and Shawn fell on his knees. Sir Thorn and even Selvaggia widened their eyes. In front of them was Mizutaro, changed.

The Dewott had been completely stripped of his samurai attire, but that was far from the only thing Cipher had dealt with: gone was his bright smile, his joyful and friendly disposition, his whole _being_. He just stood there, emotionless and unnaturally still, awaiting orders. Not even Sir Thorn or Selvaggia could look straight at him.

Shawn swallowed, hand extended towards him. "Mizutaro?"

The Dewott didn't respond.

Shawn's head faced downward. "SD0016?"

The Shadow Pokémon turned its head up, still wordless.

Shawn lost all words, staring down at Jeff's Pokémon. Mizutaro was no more, all that was left was SD0016, Cipher's tool. _His_ tool.

He fell on his knees, punching the ground as he let tears run down his cheeks. He wanted to yell, but he just couldn't, so he just stood there, observing what he caused. It was all his fault. All of it.

Shawn hugged Mizutaro, holding him tight.

"I'm sorry, Mizutaro! I didn't want this!" Shawn hugged him even tighter. SD0016 didn't reply at all as he sobbed on him.

"I am sorry..."

* * *

 **This was a pretty dark one-shot overall, but given it was pretty much a villain episode it was inevitable. My aim was to give a general showcase of Cipher and how it acts with this story, and I hope to have done a good job. I plan to continue the story of Shawn and Mizutaro in further stories, and I do hope you will like it.**

 **Exol happens to be a game character, the only one in the games to have the 'Cipher Commander' class, which is only met once in XD. Shadow Mawile and Raichu also happen to be two Pokémon part of his team during their battle. The idea of wild Mandibuzz in Orre and mentions of Dakim as 'Burning Earth' come from Pokémon Reset Bloodlines: Dakim Gaiden by Shadow Ninja Koopa, a story I'd reccomend everyone to read.**

 **In any case, thanks to everyone that will read!**


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